Just a short note, but for those who have been waiting for a version of NDoc that supports .NET 2.0 assemblies, there is a separate project out on SourceForge called NDoc 2005. It is still in beta, but it may be the way to go until NDoc gets moving again. Per comments at MSDN forums, it looks like the best way to go is to download the source and recompile it yourself. The binaries (at least the GUI binary) look like they still have some issues.
Note: unfortunately, it still doesn’t completely work for me… sigh